Kras-neoantigen therapies

Abstract

Disclosed herein are compositions that include antigen-encoding nucleic acid sequences having multiple iterations of KRAS neoepitope-encoding sequences and/or lacking immunodominant epitopes. Also disclosed are nucleotides, cells, and methods associated with the compositions including their use as vaccines, such as in subjects with cancer that includes (1) a solid tumor expressing the KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA).

What is claimed is: 
     
         1 . A method for treating a subject with a disease, wherein the disease is cancer comprising (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises an antigen-encoding cassette, or a polypeptide sequence encoded by the cassette, wherein the antigen-encoding cassette comprises at least one antigen-encoding nucleic acid sequence described, from 5′ to 3′, by the formula:
   (E x -(E N   n ) y ) z    
 wherein, 
 E represents a nucleotide sequence a distinct epitope-encoding nucleic acid sequences, 
 n represents the number of separate distinct epitope-encoding nucleic acid sequences and is any integer including 0, 
 E N  represents a nucleotide sequence comprising the separate distinct epitope-encoding nucleic acid sequence for each corresponding n, 
 for each iteration of z: x=0 or 1, y=0 or 1 for each n, and at least one of x or y=1, and z=2 or greater, wherein the antigen-encoding nucleic acid sequence comprises at least two iterations of E, a given E N , or a combination thereof, and 
 at least one of the distinct epitope-encoding nucleic acid sequences comprising the at least two iterations encodes the KRAS-associated MHC class I neoepitope. 
 
     
     
         2 . A method for treating a subject with a disease, wherein the disease is cancer comprising (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises an antigen expression system, comprising:
 the antigen expression system,   wherein the antigen expression system comprises one or more vectors,   the one or more vectors comprising:   (a) a vector backbone, wherein the backbone comprises:
 (i) at least one promoter nucleotide sequence, and 
 (ii) optionally, at least one polyadenylation (poly(A)) sequence; and 
   (b) a cassette, wherein the cassette comprises:
 (i) at least one antigen-encoding nucleic acid sequence, comprising:
 (I) an epitope-encoding nucleic acid sequence encoding the KRAS-associated MHC class I neoepitope, and
 wherein each of the epitope-encoding nucleic acid sequences comprises; 
 (A) optionally, a 5′ linker sequence, and 
 (B) optionally, a 3′ linker sequence; 
 
 
 (ii) optionally, a second promoter nucleotide sequence operably linked to the antigen-encoding nucleic acid sequence; and 
 (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; 
 (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and 
 (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, 
   wherein if the second promoter nucleotide sequence is absent, the antigen-encoding nucleic acid sequence is operably linked to the at least one promoter nucleotide sequence, and   wherein the at least one antigen-encoding nucleic acid sequence comprises at least two iterations of the epitope-encoding nucleic acid sequence encoding the KRAS-associated MHC class I neoepitope.   
     
     
         3 . The method of  any one of the above claims , wherein the epitope-encoding nucleic acid sequence is derived from a tumor of the subject with cancer or from a cell or sample of the infected subject. 
     
     
         4 . The method  any one of the above claims , wherein the epitope-encoding nucleic acid sequence are not derived from a tumor of the subject with cancer or from a cell or sample of the infected subject. 
     
     
         5 . A method for stimulating an immune response in a subject with cancer, wherein the cancer comprises (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises an antigen-encoding cassette, or a polypeptide sequence encoded by the cassette, wherein the antigen-encoding cassette comprises at least one antigen-encoding nucleic acid sequence described, from 5′ to 3′, by the formula:
   (E x -(E N   n ) y ) z    
 wherein, 
 E represents a nucleotide sequence comprising a distinct epitope-encoding nucleic acid sequences, 
 n represents the number of separate distinct epitope-encoding nucleic acid sequences and is any integer including 0, 
 E N  represents a nucleotide sequence comprising the separate distinct epitope-encoding nucleic acid sequence for each corresponding n, 
 for each iteration of z: x=0 or 1, y=0 or 1 for each n, and at least one of x or y=1, and z=2 or greater, wherein the antigen-encoding nucleic acid sequence comprises at least two iterations of E, a given E N , or a combination thereof, and 
 at least one of the distinct epitope-encoding nucleic acid sequences comprising the at least two iterations encodes the KRAS-associated MHC class I neoepitope. 
 
     
     
         6 . A method for stimulating an immune response in a subject with cancer, wherein the cancer comprises (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises:
 an antigen expression system, comprising:   the antigen expression system,   wherein the antigen expression system comprises one or more vectors,   the one or more vectors comprising:   (a) a vector backbone, wherein the backbone comprises:
 (i) at least one promoter nucleotide sequence, and 
 (ii) optionally, at least one polyadenylation (poly(A)) sequence; and 
   (b) a cassette, wherein the cassette comprises:   (i) at least one antigen-encoding nucleic acid sequence, comprising:
 (I) an epitope-encoding nucleic acid sequence encoding the KRAS-associated MHC class I neoepitope, and
 wherein each of the epitope-encoding nucleic acid sequences comprises; 
 (A) optionally, a 5′ linker sequence, and 
 (B) optionally, a 3′ linker sequence; 
 
 (ii) optionally, a second promoter nucleotide sequence operably linked to the antigen-encoding nucleic acid sequence; and 
 (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; 
 (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and 
 (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, 
   wherein if the second promoter nucleotide sequence is absent, the antigen-encoding nucleic acid sequence is operably linked to the at least one promoter nucleotide sequence, and   wherein the at least one antigen-encoding nucleic acid sequence comprises at least two iterations of at least one of the epitope-encoding nucleic acid sequences encoding the KRAS-associated MHC class I neoepitope.   
     
     
         7 . The method of  any one of the above claims , wherein the subject expresses at least one HLA allele predicted or known to present the at least one epitope sequence, optionally wherein the at least one epitope sequence predicted or known to be presented comprises the KRAS-associated MHC class I neoepitope. 
     
     
         8 . The method of  any one of the above claims , wherein the subject expresses at least one HLA allele predicted or known to present the at least one epitope sequence, and wherein the at least one epitope sequence comprises an epitope known or suspected to be presented by MHC class I on a surface of a cell, optionally wherein the at least one epitope sequence predicted or known to be presented comprises the KRAS-associated MHC class I neoepitope. 
     
     
         9 . The method of  claim 8 , wherein the surface of the cell is a tumor cell surface. 
     
     
         10 . A method for inducing an immune response in a subject with cancer, wherein the cancer comprises (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises an antigen-encoding cassette, or a polypeptide sequence encoded by the cassette, wherein the antigen-encoding cassette comprises at least one antigen-encoding nucleic acid sequence described, from 5′ to 3′, by the formula:
   (E x -(E N   n ) y ) z    
 wherein, 
 E represents a nucleotide sequence comprising a distinct epitope-encoding nucleic acid sequences, 
 n represents the number of separate distinct epitope-encoding nucleic acid sequences and is any integer including 0, 
 E N  represents a nucleotide sequence comprising the separate distinct epitope-encoding nucleic acid sequence for each corresponding n, 
 for each iteration of z: x=0 or 1, y=0 or 1 for each n, and at least one of x or y=1, and z=2 or greater, wherein the antigen-encoding nucleic acid sequence comprises at least two iterations of E, a given E N , or a combination thereof, and 
 at least one of the distinct epitope-encoding nucleic acid sequences comprising the at least two iterations encodes a KRAS-associated MHC class I neoepitope. 
 
     
     
         11 . A method for inducing an immune response in a subject with cancer, wherein the cancer comprises (1) a solid tumor expressing a KRAS-associated MHC class I neoepitope, (2) colorectal cancer (CRC), (3) non-small cell lung cancer (NSCLC), and/or (4) pancreatic ductal adenocarcinoma (PDA), the method comprising administering to the subject an antigen-based vaccine to the subject, wherein the antigen-based vaccine comprises:
 an antigen expression system, comprising:   the antigen expression system,   wherein the antigen expression system comprises one or more vectors,   the one or more vectors comprising:   (a) a vector backbone, wherein the backbone comprises:
 (i) at least one promoter nucleotide sequence, and 
 (ii) optionally, at least one polyadenylation (poly(A)) sequence; and 
   (b) a cassette, wherein the cassette comprises:
 (i) at least one antigen-encoding nucleic acid sequence, comprising:
 (I) an epitope-encoding nucleic acid sequence encoding the KRAS-associated MHC class I neoepitope, and
 wherein each of the epitope-encoding nucleic acid sequences comprises; 
 (A) optionally, a 5′ linker sequence, and 
 (B) optionally, a 3′ linker sequence; 
 
 
 (ii) optionally, a second promoter nucleotide sequence operably linked to the antigen-encoding nucleic acid sequence; and 
 (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; 
 (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and 
 (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, 
   wherein if the second promoter nucleotide sequence is absent, the antigen-encoding nucleic acid sequence is operably linked to the at least one promoter nucleotide sequence,   wherein the at least one antigen-encoding nucleic acid sequence comprises at least two iterations of the epitope-encoding nucleic acid sequence encoding the KRAS-associated MHC class I neoepitope, and   wherein the subject expresses at least one HLA allele predicted or known to present the at least one KRAS-associated MHC class I neoepitope.   
     
     
         12 . The method of  any one of the above claims , wherein the antigen-based vaccine is administered as a priming dose. 
     
     
         13 . The method of  any one of the above claims , wherein the antigen-based vaccine is administered as one or more boosting doses. 
     
     
         14 . The method of  claim 13 , wherein the boosting dose is different than the priming dose. 
     
     
         15 . The method of  claim 14 , wherein:
 a) the priming dose comprises a chimpanzee adenovirus vector and the boosting dose comprises an alphavirus vector; or   b) the priming dose comprises an alphavirus vector and the boosting dose comprises a chimpanzee adenovirus vector.   
     
     
         16 . The method of  claim 13 , wherein the boosting dose is the same as the priming dose. 
     
     
         17 . The method of any one of  claims 13-16 , wherein the injection site of the one or more boosting doses is as close as possible to the injection site of the priming dose. 
     
     
         18 . The method of  any one of the above method claims , further comprising determining or having determined the HLA-haplotype of the subject. 
     
     
         19 . The method of  any one of the above method claims , wherein the antigen-based vaccine is administered intramuscularly (IM), intradermally (ID), subcutaneously (SC), or intravenously (IV). 
     
     
         20 . The method of  any one of the above method claims , wherein the antigen-based vaccine is administered intramuscularly (IM). 
     
     
         21 . The method of  claim 20 , wherein the IM administration is administered at separate injection sites. 
     
     
         22 . The method of  claim 21 , wherein the separate injection sites are in opposing deltoid muscles. 
     
     
         23 . The method of  claim 22 , wherein the separate injection sites are in gluteus or rectus femoris sites on each side. 
     
     
         24 . The method of  any of the above claims , wherein the KRAS-associated MHC class I neoepitope or the KRAS mutation comprises a KRAS G12C mutation, a KRAS G12V mutation, a KRAS G12D mutation, or a KRAS Q61H mutation. 
     
     
         25 . The method of  any of the above claims , wherein the KRAS-associated MHC class I neoepitope or the KRAS mutation comprises any one of the amino acid sequence shown in SEQ ID NOs: 75-82. 
     
     
         26 . The method of  any of the above claims , wherein the antigen-encoding cassette comprises each of the amino acid sequence shown in SEQ ID NOs: 75-82. 
     
     
         27 . The method or composition of  any of the above claims , wherein the antigen-encoding cassette comprises two or more iterations of each of the amino acid sequence shown in SEQ ID NOs: 75-82, optionally comprising 4 iterations of each of the amino acid sequence shown in SEQ ID NOs: 75-82. 
     
     
         28 . The method of  any of the above claims , wherein the KRAS-associated MHC class I neoepitope or the KRAS mutation comprises the amino acid sequence shown in SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, or SEQ ID NO: 60. 
     
     
         29 . The method of  any of the above claims , wherein the epitope-encoding nucleic acid sequences comprises two or more distinct epitope-encoding nucleic acid sequences independently encoding a distinct KRAS-associated MHC class I neoepitope or a distinct KRAS mutation. 
     
     
         30 . The method of  any of the above claims , wherein each of the epitope-encoding nucleic acid sequences independently encodes a distinct KRAS-associated MHC class I neoepitope or a distinct KRAS mutation. 
     
     
         31 . The method of  any of the above claims , wherein the epitope-encoding nucleic acid sequences comprises two or more distinct epitope-encoding nucleic acid sequences independently encoding a KRAS G12C mutation, a KRAS G12V mutation, a KRAS G12D mutation, or a KRAS Q61H mutation. 
     
     
         32 . The method of  any of the above claims , wherein the epitope-encoding nucleic acid sequences independently encodes each of a KRAS G12C mutation, a KRAS G12V mutation, and a KRAS G12D mutation, and optionally a KRAS Q61H mutation. 
     
     
         33 . The method of  any of the above claims , wherein the antigen-encoding nucleic acid sequence encodes a peptide comprising the amino acid sequence shown in SEQ ID NO: 64 or SEQ ID NO: 65. 
     
     
         34 . The method of  any of the above claims , wherein the cassette does not encode an immunodominant MHC class I epitope that:
 (1) stimulates a 5-fold or greater immune response when administered in a vaccine composition to a subject relative to another MHC class I epitope encoded in the cassette and capable of stimulating an immune response in the subject, and/or   (2) reduces an immune response to another MHC class I epitope encoded in the cassette when administered in a vaccine composition to a subject relative to an immune response when the other MHC class I epitope is administered in the absence of the immunodominant MHC class I epitope, optionally wherein the immune response is reduced to below a limit of detection and/or wherein the immune response is not a therapeutically effective response.   
     
     
         35 .  Any one of the above method claims , wherein the cancer comprises a solid tumor expressing a KRAS-associated and/or a NRAS-associated MHC class I neoepitope. 
     
     
         36 . The method of  claim 35 , wherein the KRAS-associated and/or the NRAS-associated MHC class I neoepitope comprises a mutation selected from the group consisting of: KRAS_G12C, NRAS_G12C, KRAS_G12D, NRAS_G12D, KRAS_G12V, NRAS_G12V, KRAS_Q61H, and NRAS_Q61H. 
     
     
         37 .  Any one of the above method claims , wherein the cancer comprises colorectal cancer (CRC). 
     
     
         38 .  Any one of the above method claims , wherein the cancer comprises non-small cell lung cancer (NSCLC). 
     
     
         39 .  Any one of the above method claims , wherein the cancer comprises pancreatic ductal adenocarcinoma (PDA). 
     
     
         40 .  Any one of the above method claims , wherein the antigen-based vaccine or the one or more boosting doses is administered every 4 weeks (Q4W). 
     
     
         41 .  Any one of the above method claims , wherein the antigen-based vaccine or the one or more boosting doses is administered every 8 weeks (Q8W). 
     
     
         42 .  Any one of the above method claims , wherein the antigen-based vaccine or the one or more boosting doses is administered monthly. 
     
     
         43 .  Any one of the above method claims , wherein the antigen-based vaccine or the one or more boosting doses is administered every two months. 
     
     
         44 .  Any one of the above method claims , wherein the method comprises administering to the subject a composition for delivery of a self-replicating alphavirus-based expression system and administering to the subject a composition for delivery of a chimpanzee adenovirus (ChAdV)-based expression system, and
 wherein the composition for delivery of the ChAdV-based expression system is administered as a priming dose and the composition for delivery of the self-replicating alphavirus-based expression system is administered as one or more boosting doses.   
     
     
         45 . The method of  any one of the above claims , wherein two or more boosting doses are administered. 
     
     
         46 . The method of  any one of the above claims , wherein 1, 2, 3, 4, 5, 6, 7, or 8 boosting doses are administered. 
     
     
         47 . The method of  any one of the above claims , wherein the ChAdV-based expression system is further administered as a boosting dose. 
     
     
         48 . The method of  claim 47 , wherein the ChAdV-based boosting dose is only administered as a single boosting dose. 
     
     
         49 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or about day 140 after the priming dose of the ChAdV-based expression system. 
     
     
         50 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or about week 20 after the priming dose of the ChAdV-based expression system. 
     
     
         51 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or about month 5 after the priming dose of the ChAdV-based expression system. 
     
     
         52 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or after day 140 after the priming dose of the ChAdV-based expression system. 
     
     
         53 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or after week 20 after the priming dose of the ChAdV-based expression system. 
     
     
         54 . The method of  claim 47 or 48 , wherein the ChAdV-based expression system is administered as the boosting dose on or after month 5 after the priming dose of the ChAdV-based expression system. 
     
     
         55 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two boosting doses. 
     
     
         56 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least 28 days apart. 
     
     
         57 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least 4 weeks (Q4W) apart. 
     
     
         58 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least one month apart. 
     
     
         59 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least 56 days apart. 
     
     
         60 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least 8 weeks (Q8W) apart. 
     
     
         61 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two or more boosting doses at least 2 months apart. 
     
     
         62 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two boosting doses on or about days 28 and 84 after the priming dose of the ChAdV-based expression system. 
     
     
         63 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two boosting doses on or about weeks 4 and 12 after the priming dose of the ChAdV-based expression system. 
     
     
         64 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least two boosting doses on or about months 1 and 3 after the priming dose of the ChAdV-based expression system. 
     
     
         65 . The method of  any one of the above claims , wherein the self-replicating alphavirus-based expression system is administered as at least four boosting doses. 
     
     
         66 . The method of  claim 65 , wherein the self-replicating alphavirus-based expression system is administered on or about days 28, 84, 196, and 252 relative to the priming dose of the ChAdV-based expression system. 
     
     
         67 . The method of  claim 65 , wherein the self-replicating alphavirus-based expression system is administered on or about weeks 4, 12, 28, and 40 relative to the priming dose of the ChAdV-based expression system. 
     
     
         68 . The method of  claim 65 , wherein the self-replicating alphavirus-based expression system is administered on or about months 1, 3, 7, and 10 relative to the priming dose of the ChAdV-based expression system. 
     
     
         69 . The method of  any one of the above claims , the method further comprising administration of one or more immune modulators, optionally wherein the immune modulator is administered before, concurrently with, or after administration of the composition or pharmaceutical composition. 
     
     
         70 . The method of  claim 55 , wherein the one or more immune modulators are selected from the group consisting of: an anti-CTLA4 antibody or an antigen-binding fragment thereof, an anti-PD-1 antibody or an antigen-binding fragment thereof, an anti-PD-L1 antibody or an antigen-binding fragment thereof, an anti-4-1BB antibody or an antigen-binding fragment thereof, or an anti-OX-40 antibody or an antigen-binding fragment thereof. 
     
     
         71 . The method of  claim 56 or 57 , wherein the immune modulator is administered intravenously (IV), intramuscularly (IM), intradermally (ID), or subcutaneously (SC). 
     
     
         72 . The method of  claim 58 , wherein the subcutaneous administration is near the site of the composition or pharmaceutical composition administration or in close proximity to one or more vector or composition draining lymph nodes. 
     
     
         73 . The method of any one  claims 56-59 , wherein the method comprises administration of an anti-CTLA-4 antibody or an antigen-binding fragment thereof only with the priming dose and the first boosting dose. 
     
     
         74 . The method of  claim 60 , wherein the anti-CTLA-4 antibody comprises ipilimumab. 
     
     
         75 . The method of  claim 61 , wherein the ipilimumab is administered at a dose of 30 mg subcutaneously. 
     
     
         76 . The method of any one of  claims 56-62 , wherein the method comprises administration of an anti-PD-L1 antibody or an antigen-binding fragment thereof every 4 weeks (Q4W), optionally comprising. 
     
     
         77 . The method of  claim 63 , wherein the anti-PD-L1 antibody comprises atezolizumab or nivolumab. 
     
     
         78 . The method of  claim 64 , wherein the atezolizumab is administered at a dose of 1680 mg intravenously or the nivolumab is administered at a dose of 480 mg intravenously. 
     
     
         79 . The method of any one of  claims 56-65 , wherein the method comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 administrations of one or more of the immune modulators. 
     
     
         80 . The method of any one of  claims 56-65 , wherein the method comprises at least 13 administrations of the anti-PD-L1 antibody. 
     
     
         81 . The method of any one of  claims 56-67 , wherein the one or more immune modulators are selected from the group consisting of: atezolizumab, nivolumamb, cemiplimab, and ipilimumab. 
     
     
         82 . Any one of the above method or composition claims, wherein
 the KRAS-associated MHC class I neoepitope comprising a KRAS G12C mutation is selected from the group consisting of: VVVGACGVGK (SEQ ID NO: 75), KLVVVGACGV (SEQ ID NO: 76), and GACGVGKSAL (SEQ ID NO: 93);   the KRAS-associated MHC class I neoepitope comprising a KRAS G12D mutation is selected from the group consisting of: VVGADGVGK (SEQ ID NO: 77), VVVGADGVGK (SEQ ID NO: 78), KLVVVGADGV (SEQ ID NO: 94), and GADGVGKSAL (SEQ ID NO: 95);   the KRAS-associated MHC class I neoepitope comprising a KRAS G12V mutation is selected from the group consisting of: VVGAVGVGK (SEQ ID NO: 79), VVVGAVGVGK (SEQ ID NO: 81), AVGVGKSAL (SEQ ID NO: 80), and GAVGVGKSAL (SEQ ID NO: 96).   
     
     
         83 . Any one of the above method or composition claims, wherein the KRAS-associated MHC class I neoepitope comprising a KRAS G12C mutation is selected from the group consisting of: VVVGACGVGK (SEQ ID NO: 75), KLVVVGACGV (SEQ ID NO: 76), and GACGVGKSAL (SEQ ID NO: 93). 
     
     
         84 . Any one of the above method or composition claims, wherein the KRAS-associated MHC class I neoepitope comprising a KRAS G12D mutation is selected from the group consisting of: VVGADGVGK (SEQ ID NO: 77), VVVGADGVGK (SEQ ID NO: 78), KLVVVGADGV (SEQ ID NO: 94), and GADGVGKSAL (SEQ ID NO: 95). 
     
     
         85 . Any one of the above method or composition claims, wherein the KRAS-associated MHC class I neoepitope comprising a KRAS G12V mutation is selected from the group consisting of: VVGAVGVGK (SEQ ID NO: 79), VVVGAVGVGK (SEQ ID NO: 81), AVGVGKSAL (SEQ ID NO: 80), and GAVGVGKSAL (SEQ ID NO: 96). 
     
     
         86 . Any one of the above method or composition claims, wherein the stimulating the immune response comprises stimulating a molecular response. 
     
     
         87 . The method or composition of  claim 73 , wherein the molecular response comprises a reduction in ctDNA. 
     
     
         88 . The method or composition of  claim 74 , wherein the reduction in ctDNA is at least a 20%, at least a 30%, at least a 40%, or at least a 50% reduction in ctDNA. 
     
     
         89 . The method or composition of  claim 74 , wherein the reduction in ctDNA is at least a 30% reduction in ctDNA.